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META-PP: single interface to crucial prediction servers

V. A. Eyrich
2003 Nucleic Acids Research  
The META-PP server (http://cubic.bioc.columbia. edu/meta/) simplifies access to a battery of public protein structure and function prediction servers by providing a common and stable web-based interface  ...  At present META-PP provides access to a selected set of high-quality servers in the areas of comparative modelling, threading/fold recognition, secondary structure prediction and more specialized fields  ...  Last, and by no means least, thanks to all those who deposit their experimental data in public databases, those who maintain these databases and all the developers who make their prediction methods available  ... 
doi:10.1093/nar/gkg572 pmid:12824314 pmcid:PMC168978 fatcat:v7su4cpb5ncvrn7hmfkde6tfri

Basic protein structure prediction for the biologist: A review

M. Mihăşan
2010 Archives of Biological Sciences  
As the field of protein structure prediction continues to expand at an exponential rate, the bench-biologist might feel overwhelmed by the sheer range of available applications.  ...  This review presents the three main approaches in computational structure prediction from a non-bioinformatician's point of view and makes a selection of tools and servers freely available.  ...  Protein structure prediction: A special issue. Proteins: Structure, Function, and Genetics, 23(3), i.  ... 
doi:10.2298/abs1004857m fatcat:yp4dq55s5bbnzezhcjpv4qhlpa

State-of-the-art in membrane protein prediction

Chien Peter Chen, Burkhard Rost
2002 Applied Bioinformatics  
The best current prediction methods appear to correctly predict all membrane helices for about 50%-70% of all proteins, and to falsely predict membrane helices for about 10% of all globular proteins.  ...  Additionally, all methods tend to confuse signal peptides with membrane helices. Nonetheless, wet-lab biologists can reach into an impressive toolbox for membrane protein predictions.  ...  Acknowledgements Thanks to Jinfeng Liu (Columbia) for computer assistance and to Henry Bigelow for comments and help with β-membrane prediction methods.  ... 
pmid:15130854 fatcat:l6mto32unndspbdphio43eri6q

An in-frame complex germline mutation in the juxtamembrane intracellular domain causing RET activation in familial medullary thyroid carcinoma

Daniela Cordella, Marina Muzza, Luisella Alberti, Paolo Colombo, Pietro Travaglini, Paolo Beck-Peccoz, Laura Fugazzola, Luca Persani
2006 Endocrine-Related Cancer  
This in-frame complex rearrangement leads to an Asn to Lys change (Lys666Asn) and to a Ser insertion.  ...  Single base pair missense mutations in the extracellular Cys-rich domain are responsible for most MEN2A and familial MTC (FMTC) cases.  ...  Acknowledgements The authors are grateful to Dr Italia Bongarzone and Piera Mondellini (Istituto dei Tumori, Milan), for donating plasmids carrying Ret9-WT and Ret9-C634R and for helpful discussion.  ... 
doi:10.1677/erc.1.01144 pmid:16954442 fatcat:dge4ibfhfrbezlwejdzch76u3a

Phylogenetic Analysis [chapter]

An Introduction to Computational Biochemistry  
To request 3D structure analysis by multiservers via META-PP submission at the PredictProtein site, click Submit Requests to META-PP to open the submission form.  ...  Because no single prediction method is perfect, it is advisable to submit the query sequence to several different computational programs for the gene prediction.  ...  Approaches to protein modeling by the use of two programs (Swiss-Pdb Viewer and KineMage) and two online servers (B and CE) are described.  ... 
doi:10.1002/0471223840.ch13 fatcat:nipg4bxrevau3efb6bagqscufy